endoreg-db 0.6.3__py3-none-any.whl → 0.8.1__py3-none-any.whl

endoreg_db/data/finding_intervention/endoscopy.yaml

@@ -1,138 +1,43 @@
-- model: endoreg_db.finding_intervention
-  fields:
-    name: "colon-lesion-polypectomy-cold-snare"
-    description: "Cold snare polypectomy is a technique used to remove small polyps from the colon. It is performed using a snare wire loop that is passed through the colonoscope and used to remove the polyp by cutting it off at the base. The procedure is usually done without the need for sedation and is considered to be a safe and effective way to remove small polyps from the colon."
-    intervention_types: [
-      "therapeutic",
-      "invasive",
-    ]
-
-    required_lab_values: [
-      "hemoglobin",
-      "platelets",
-      "international_normalized_ratio",
-    ]
-
-    contraindications: [
-      "anticoagulation-therapeutic",
-      "thrombocytopenia-severe"
-    ]
+# --- Begin kept interventions ---
 
 - model: endoreg_db.finding_intervention
   fields:
-    name: "colon-lesion-polypectomy-hot-snare"
-    description: "Hot snare polypectomy is a technique used to remove small polyps from the colon. It is performed using a snare wire loop that is passed through the colonoscope and used to remove the polyp by cutting it off at the base. The procedure is usually done without the need for sedation and is considered to be a safe and effective way to remove small polyps from the colon."
-    intervention_types: [
-      "therapeutic",
-      "invasive",
-    ]
-
-    required_lab_values: [
-      "hemoglobin",
-      "platelets",
-      "international_normalized_ratio",
-    ]
-
-    contraindications: [
-      "anticoagulation-therapeutic",
-      "thrombocytopenia-severe"
-    ]
-
-- model: endoreg_db.finding_intervention
-  fields:
-    name: "colon-lesion-injection-liftup"
-    description: "Lift-up injection is a technique used to lift up a lesion in the colon. It is performed by injecting a solution under the lesion to create a cushion of fluid that lifts the lesion away from the colon wall. This allows the lesion to be removed more easily and reduces the risk of complications during the procedure."
-    intervention_types: [
-      "diagnostic",
-      "invasive",
-    ]
-
-    required_lab_values: [
-      "hemoglobin",
-      "platelets",
-      "international_normalized_ratio",
-    ]
-
-    contraindications: [
-    ]
-
-- model: endoreg_db.finding_intervention
-  fields:
-    name: "colon-lesion-injection-vasoactive"
-    description: "Vasoactive injection is a technique used to reduce bleeding from a lesion in the colon. It is performed by injecting a solution into the lesion that causes the blood vessels to constrict, reducing the flow of blood to the area. This can help to stop bleeding and make it easier to remove the lesion during the procedure."
-    intervention_types: [
-      "therapeutic",
-      "invasive",
-    ]
-
+    name: percutaneous_transhepatic_cholangiography
+    description: "TODO: Add description"
+    intervention_types: []
     required_lab_values: []
     contraindications: []
-
 - model: endoreg_db.finding_intervention
   fields:
-    name: "colon-lesion-biopsy"
-    description: "Biopsy is a technique used to take a small sample of tissue from a lesion in the colon. It is performed by inserting a small instrument through the colonoscope and removing a small piece of tissue from the lesion. The tissue sample is then sent to a laboratory for analysis to determine if the lesion is cancerous or benign."
-    intervention_types: [
-      "diagnostic",
-      "invasive",
-    ]
-
+    name: sonography_guided_liver_punction
+    description: "TODO: Add description"
+    intervention_types: []
     required_lab_values: []
-    contraindications: [
-      "anticoagulation-therapeutic",
-      "thrombocytopenia-severe"
-    ]
-
+    contraindications: []
 - model: endoreg_db.finding_intervention
   fields:
-    name: "colon-lesion-emr"
-    description: "Endoscopic mucosal resection (EMR) is a technique used to remove large polyps or early-stage cancers from the colon. It is performed by injecting a solution under the lesion to create a cushion of fluid that lifts the lesion away from the colon wall. A snare wire loop is then used to remove the lesion by cutting it off at the base. The procedure is usually done under sedation and is considered to be a safe and effective way to remove large polyps or early-stage cancers from the colon."
-    intervention_types: [
-      "therapeutic",
-      "invasive",
-    ]
-
-    required_lab_values: [
-      "hemoglobin",
-      "platelets",
-      "international_normalized_ratio",
-    ]
-
-    contraindications: [
-      "anticoagulation-therapeutic",
-      "thrombocytopenia-severe"
-    ]
-
+    name: xray_guided_liver_punction
+    description: "TODO: Add description"
+    intervention_types: []
+    required_lab_values: []
+    contraindications: []
 - model: endoreg_db.finding_intervention
   fields:
-    name: "colon-lesion-esd"
-    description: "Endoscopic submucosal dissection (ESD) is a technique used to remove large polyps or early-stage cancers from the colon. It is performed by injecting a solution under the lesion to create a cushion of fluid that lifts the lesion away from the colon wall. A snare wire loop is then used to remove the lesion by cutting it off at the base. The procedure is usually done under sedation and is considered to be a safe and effective way to remove large polyps or early-stage cancers from the colon."
-    intervention_types: [
-      "therapeutic",
-      "invasive",
-    ]
-
-    required_lab_values: [
-      "hemoglobin",
-      "platelets",
-      "international_normalized_ratio",
-    ]
-
-    contraindications: [
-      "anticoagulation-therapeutic",
-      "thrombocytopenia-severe"
-    ]
-
+    name: percutaneous_transhepatic_biliary_drainage
+    description: "TODO: Add description"
+    intervention_types: []
+    required_lab_values: []
+    contraindications: []
 - model: endoreg_db.finding_intervention
   fields:
-    name: "colon-lesion-clip"
-    description: "Clip closure is a technique used to close a defect in the colon wall after a polyp has been removed. It is performed by placing a small metal clip over the defect to seal it and prevent bleeding or perforation. The clip is left in place until the defect has healed, usually within a few days."
-    intervention_types: [
-      "therapeutic",
-      "invasive",
-      "foreign_body",
-    ]
-
+    name: biliary_stent
+    description: "TODO: Add description"
+    intervention_types: []
     required_lab_values: []
     contraindications: []
+# --- End kept interventions ---
 
+# --- Removed interventions moved to other files ---
+# Removed: all items with names starting with "egd_"
+# Removed: all items with names starting with "erc", "ercp", "erp"
+# Removed: all items with names starting with "endosonography_upper_gi_"

endoreg_db/data/finding_intervention/endoscopy_colonoscopy.yaml

@@ -0,0 +1,168 @@
+- model: endoreg_db.finding_intervention
+  fields:
+    name: colon_lesion_polypectomy_cold_snare
+    description:
+      Cold snare polypectomy is a technique used to remove small polyps
+      from the colon. It is performed using a snare wire loop that is passed through
+      the colonoscope and used to remove the polyp by cutting it off at the base.
+      The procedure is usually done without the need for sedation and is considered
+      to be a safe and effective way to remove small polyps from the colon.
+    intervention_types:
+      - therapeutic
+      - invasive
+    required_lab_values:
+      - hemoglobin
+      - platelets
+      - international_normalized_ratio
+    contraindications:
+      - anticoagulation-therapeutic
+      - thrombocytopenia-severe
+- model: endoreg_db.finding_intervention
+  fields:
+    name: colon_lesion_polypectomy_hot_snare
+    description:
+      Hot snare polypectomy is a technique used to remove small polyps
+      from the colon. It is performed using a snare wire loop that is passed through
+      the colonoscope and used to remove the polyp by cutting it off at the base.
+      The procedure is usually done without the need for sedation and is considered
+      to be a safe and effective way to remove small polyps from the colon.
+    intervention_types:
+      - therapeutic
+      - invasive
+    required_lab_values:
+      - hemoglobin
+      - platelets
+      - international_normalized_ratio
+    contraindications:
+      - anticoagulation-therapeutic
+      - thrombocytopenia-severe
+- model: endoreg_db.finding_intervention
+  fields:
+    name: colon_lesion_injection_liftup
+    description:
+      Lift-up injection is a technique used to lift up a lesion in the
+      colon. It is performed by injecting a solution under the lesion to create a
+      cushion of fluid that lifts the lesion away from the colon wall. This allows
+      the lesion to be removed more easily and reduces the risk of complications during
+      the procedure.
+    intervention_types:
+      - diagnostic
+      - invasive
+    required_lab_values:
+      - hemoglobin
+      - platelets
+      - international_normalized_ratio
+    contraindications: []
+- model: endoreg_db.finding_intervention
+  fields:
+    name: colon_lesion_injection_vasoactive
+    description:
+      Vasoactive injection is a technique used to reduce bleeding from
+      a lesion in the colon. It is performed by injecting a solution into the lesion
+      that causes the blood vessels to constrict, reducing the flow of blood to the
+      area. This can help to stop bleeding and make it easier to remove the lesion
+      during the procedure.
+    intervention_types:
+      - therapeutic
+      - invasive
+    required_lab_values: []
+    contraindications: []
+- model: endoreg_db.finding_intervention
+  fields:
+    name: colon_lesion_biopsy
+    description:
+      Biopsy is a technique used to take a small sample of tissue from
+      a lesion in the colon. It is performed by inserting a small instrument through
+      the colonoscope and removing a small piece of tissue from the lesion. The tissue
+      sample is then sent to a laboratory for analysis to determine if the lesion
+      is cancerous or benign.
+    intervention_types:
+      - diagnostic
+      - invasive
+    required_lab_values: []
+    contraindications:
+      - anticoagulation-therapeutic
+      - thrombocytopenia-severe
+- model: endoreg_db.finding_intervention
+  fields:
+    name: colon_lesion_emr
+    description:
+      Endoscopic mucosal resection (EMR) is a technique used to remove
+      large polyps or early-stage cancers from the colon. It is performed by injecting
+      a solution under the lesion to create a cushion of fluid that lifts the lesion
+      away from the colon wall. A snare wire loop is then used to remove the lesion
+      by cutting it off at the base. The procedure is usually done under sedation
+      and is considered to be a safe and effective way to remove large polyps or early-stage
+      cancers from the colon.
+    intervention_types:
+      - therapeutic
+      - invasive
+    required_lab_values:
+      - hemoglobin
+      - platelets
+      - international_normalized_ratio
+    contraindications:
+      - anticoagulation-therapeutic
+      - thrombocytopenia-severe
+- model: endoreg_db.finding_intervention
+  fields:
+    name: colon_lesion_esd
+    description:
+      Endoscopic submucosal dissection (ESD) is a technique used to remove
+      large polyps or early-stage cancers from the colon. It is performed by injecting
+      a solution under the lesion to create a cushion of fluid that lifts the lesion
+      away from the colon wall. A snare wire loop is then used to remove the lesion
+      by cutting it off at the base. The procedure is usually done under sedation
+      and is considered to be a safe and effective way to remove large polyps or early-stage
+      cancers from the colon.
+    intervention_types:
+      - therapeutic
+      - invasive
+    required_lab_values:
+      - hemoglobin
+      - platelets
+      - international_normalized_ratio
+    contraindications:
+      - anticoagulation-therapeutic
+      - thrombocytopenia-severe
+- model: endoreg_db.finding_intervention
+  fields:
+    name: colon_lesion_clip
+    description:
+      Clip closure is a technique used to close a defect in the colon wall
+      after a polyp has been removed. It is performed by placing a small metal clip
+      over the defect to seal it and prevent bleeding or perforation. The clip is
+      left in place until the defect has healed, usually within a few days.
+    intervention_types:
+      - therapeutic
+      - invasive
+      - foreign_body
+    required_lab_values: []
+    contraindications: []
+- model: endoreg_db.finding_intervention
+  fields:
+    name: colon_lesion_over_the_scope_clip
+    description:
+      Over-the-scope clip (OTSC) is a clipping system used to close defects
+      in the GI tract.
+    intervention_types:
+      - therapeutic
+      - invasive
+    required_lab_values: []
+    contraindications: []
+- model: endoreg_db.finding_intervention
+  fields:
+    name: colon_lesion_eftr
+    description:
+      Endoscopic full-thickness resection (EFTR) is a technique used to
+      remove lesions in the colon.
+    intervention_types:
+      - therapeutic
+      - invasive
+    required_lab_values:
+      - hemoglobin
+      - platelets
+      - international_normalized_ratio
+    contraindications:
+      - anticoagulation-therapeutic
+      - thrombocytopenia-severe

endoreg_db/data/finding_intervention/endoscopy_egd.yaml

@@ -0,0 +1,128 @@
+- model: endoreg_db.finding_intervention
+  fields:
+    name: egd_lesion_biopsy
+    # ...existing code...
+- model: endoreg_db.finding_intervention
+  fields:
+    name: egd_hp_biopsy
+    # ...existing code...
+- model: endoreg_db.finding_intervention
+  fields:
+    name: egd_lesion_injection_vasoactive
+    # ...existing code...
+- model: endoreg_db.finding_intervention
+  fields:
+    name: egd_lesion_clip
+    # ...existing code...
+- model: endoreg_db.finding_intervention
+  fields:
+    name: egd_lesion_over_the_scope_clip
+    # ...existing code...
+- model: endoreg_db.finding_intervention
+  fields:
+    name: egd_varice_band_ligation
+    # ...existing code...
+- model: endoreg_db.finding_intervention
+  fields:
+    name: egd_varice_sclerotherapy
+    # ...existing code...
+- model: endoreg_db.finding_intervention
+  fields:
+    name: egd_argon_plasma_coagulation
+    # ...existing code...
+- model: endoreg_db.finding_intervention
+  fields:
+    name: egd_percutaneous_gastroenterostomy
+    # ...existing code...
+- model: endoreg_db.finding_intervention
+  fields:
+    name: egd_percutaneous_jejunostomy
+    # ...existing code...
+- model: endoreg_db.finding_intervention
+  fields:
+    name: egd_clip
+    # ...existing code...
+- model: endoreg_db.finding_intervention
+  fields:
+    name: egd_varicosis_band_ligation
+    # ...existing code...
+- model: endoreg_db.finding_intervention
+  fields:
+    name: egd_varicosis_sclerotherapy
+    # ...existing code...
+- model: endoreg_db.finding_intervention
+  fields:
+    name: egd_injection_vasoactive
+    # ...existing code...
+- model: endoreg_db.finding_intervention
+  fields:
+    name: egd_injection_varicosis
+    # ...existing code...
+- model: endoreg_db.finding_intervention
+  fields:
+    name: egd_lesion_polypectomy_cold_snare
+    # ...existing code...
+- model: endoreg_db.finding_intervention
+  fields:
+    name: egd_lesion_polypectomy_hot_snare
+    # ...existing code...
+- model: endoreg_db.finding_intervention
+  fields:
+    name: egd_lesion_polypectomy_forceps
+    # ...existing code...
+- model: endoreg_db.finding_intervention
+  fields:
+    name: egd_lesion_injection_liftup
+    # ...existing code...
+- model: endoreg_db.finding_intervention
+  fields:
+    name: egd_lesion_emr
+    # ...existing code...
+- model: endoreg_db.finding_intervention
+  fields:
+    name: egd_lesion_esd
+    # ...existing code...
+- model: endoreg_db.finding_intervention
+  fields:
+    name: egd_eftr
+    # ...existing code...
+- model: endoreg_db.finding_intervention
+  fields:
+    name: egd_poem
+    # ...existing code...
+- model: endoreg_db.finding_intervention
+  fields:
+    name: egd_stepwise_biopsy
+    # ...existing code...
+- model: endoreg_db.finding_intervention
+  fields:
+    name: egd_esophagus_injection_botox
+    # ...existing code...
+- model: endoreg_db.finding_intervention
+  fields:
+    name: egd_stenosis_dilation
+    # ...existing code...
+- model: endoreg_db.finding_intervention
+  fields:
+    name: egd_stenosis_bougie
+    # ...existing code...
+- model: endoreg_db.finding_intervention
+  fields:
+    name: egd_stenosis_balloon
+    # ...existing code...
+- model: endoreg_db.finding_intervention
+  fields:
+    name: egd_stenosis_stent
+    # ...existing code...
+- model: endoreg_db.finding_intervention
+  fields:
+    name: egd_lesion_radiofrequency_ablation
+    # ...existing code...
+- model: endoreg_db.finding_intervention
+  fields:
+    name: egd_lesion_cryotherapy
+    # ...existing code...
+- model: endoreg_db.finding_intervention
+  fields:
+    name: egd_stenosis_laser
+    # ...existing code...

endoreg_db/data/finding_intervention/endoscopy_ercp.yaml

@@ -0,0 +1,32 @@
+- model: endoreg_db.finding_intervention
+  fields:
+    name: ercp
+    # ...existing code...
+- model: endoreg_db.finding_intervention
+  fields:
+    name: ercp_sphincterotomy
+    # ...existing code...
+- model: endoreg_db.finding_intervention
+  fields:
+    name: ercp_stent
+    # ...existing code...
+- model: endoreg_db.finding_intervention
+  fields:
+    name: ercp_extraction
+    # ...existing code...
+- model: endoreg_db.finding_intervention
+  fields:
+    name: ercp_biopsy
+    # ...existing code...
+- model: endoreg_db.finding_intervention
+  fields:
+    name: erc
+    # ...existing code...
+- model: endoreg_db.finding_intervention
+  fields:
+    name: erp
+    # ...existing code...
+- model: endoreg_db.finding_intervention
+  fields:
+    name: ercp_radiofrequency_ablation
+    # ...existing code...

endoreg_db/data/finding_intervention/endoscopy_eus_lower.yaml

@@ -0,0 +1,9 @@
+# (currently no interventions)
+- model: endoreg_db.finding_intervention
+  fields:
+    name: endosonography_lower_gi_solid_lesion_fna
+
+# endosonography_lower_gi_lymph_node_fna
+- model: endoreg_db.finding_intervention
+  fields:
+    name: endosonography_lower_gi_lymph_node_fna

endoreg_db/data/finding_intervention/endoscopy_eus_upper.yaml

@@ -0,0 +1,36 @@
+- model: endoreg_db.finding_intervention
+  fields:
+    name: endosonography_upper_gi_solid_lesion_fna
+    # ...existing code...
+- model: endoreg_db.finding_intervention
+  fields:
+    name: endosonography_upper_gi_cyst_fna
+    # ...existing code...
+- model: endoreg_db.finding_intervention
+  fields:
+    name: endosonography_upper_gi_pseudocyst_fna
+    # ...existing code...
+- model: endoreg_db.finding_intervention
+  fields:
+    name: endosonography_upper_gi_biliary_drainage
+    # ...existing code...
+- model: endoreg_db.finding_intervention
+  fields:
+    name: endosonography_upper_gi_pancreatic_drainage
+    # ...existing code...
+- model: endoreg_db.finding_intervention
+  fields:
+    name: endosonography_upper_gi_cyst_gastrostomy
+    # ...existing code...
+- model: endoreg_db.finding_intervention
+  fields:
+    name: endosonography_upper_gi_pancreaticogastrostomy
+    # ...existing code...
+- model: endoreg_db.finding_intervention
+  fields:
+    name: endosonography_upper_gi_cholangioduodenostomy
+    # ...existing code...
+- model: endoreg_db.finding_intervention
+  fields:
+    name: endosonography_upper_gi_pancreaticoduodenostomy
+    # ...existing code...

endoreg_db/data/finding_morphology_classification_type/colonoscopy.yaml

@@ -1,4 +1,4 @@
-- model: endoreg_db.finding_morphology_classification_type
+- model: endoreg_db.finding_classification_type
   fields:
     name: "colon_lesion_size"
     name_de: "Größenklassifikation Kolonläsion"
@@ -11,7 +11,7 @@
       "tumor"
     ]
 
-- model: endoreg_db.finding_morphology_classification_type
+- model: endoreg_db.finding_classification_type
   fields:
     name: "colon_lesion_shape"
     name_de: "Formklassifikation Kolonläsion"
@@ -24,7 +24,7 @@
       "tumor"
     ]
 
-- model: endoreg_db.finding_morphology_classification_type
+- model: endoreg_db.finding_classification_type
   fields:
     name: "colon_lesion_surface_intact"
     name_de: "Oberflächenklassifikation Kolonläsion"
@@ -37,7 +37,7 @@
       "tumor"
     ]
 
-- model: endoreg_db.finding_morphology_classification_type
+- model: endoreg_db.finding_classification_type
   fields:
     name: "colon_lesion_planarity"
     name_de: "Planaritätsklassifikation Kolonläsion"
@@ -51,7 +51,7 @@
     ]
 
 # Circularity
-- model: endoreg_db.finding_morphology_classification_type
+- model: endoreg_db.finding_classification_type
   fields:
     name: "colon_lesion_circularity"
     name_de: "Kolonläsion - Zirkularität"
@@ -65,7 +65,7 @@
     ]
 
 # colon_lesion_advanced_imaging
-- model: endoreg_db.finding_morphology_classification_type
+- model: endoreg_db.finding_classification_type
   fields:
     name: "colon_lesion_advanced_imaging"
     name_de: "Kolonläsion - Advanced Imaging"

endoreg_db/data/finding_type/data.yaml

@@ -1,30 +1,43 @@
 - model: endoreg_db.finding_type
   fields:
     name: "macroscopic"
-    name_de: "Makroskopisch"
-    name_en: "Macroscopic"
 
 - model: endoreg_db.finding_type
   fields:
     name: "iatrogenic"
-    name_de: "Iatrogen"
-    name_en: "Iatrogenic"
 
 - model: endoreg_db.finding_type
   fields:
     name: "postinterventional_immediate"
-    name_de: "Postinterventionell unmittelbar"
-    name_en: "Postinterventional Immediate"
 
 - model: endoreg_db.finding_type
   fields:
     name: "postinterventional_delayed"
-    name_de: "Postinterventionell verzögert"
-    name_en: "Postinterventional Delayed"
 
 - model: endoreg_db.finding_type
   fields:
     name: "bleeding"
-    name_de: "Blutung"
-    name_en: "Bleeding"
 
+- model: endoreg_db.finding_type
+  fields:
+    name: "endoscopy_baseline"
+
+- model: endoreg_db.finding_type
+  fields:
+    name: "medication_related"
+    
+- model: endoreg_db.finding_type
+  fields:
+    name: "anatomy"
+
+- model: endoreg_db.finding_type
+  fields:
+    name: "anatomy_colon"
+
+- model: endoreg_db.finding_type
+  fields:
+    name: "summary"
+
+- model: endoreg_db.finding_type
+  fields:
+    name: "complication"

endoreg_db/data/gender/data.yaml

@@ -17,7 +17,7 @@
     abbreviation: "f"
 - model: endoreg_db.gender
   fields:
-    name: "mostly_femaly"
+    name: "mostly_female"
     name_de: "überwiegend weiblich"
     name_en: "mostly female"
     abbreviation: "mf"
@@ -33,3 +33,10 @@
     name_de: "andere"
     name_en: "other"
     abbreviation: "x"
+- model: endoreg_db.gender
+  fields:
+    name: "unknown"
+    name_de: "unbekannt"
+    name_en: "unknown"
+    abbreviation: "?"
+

endoreg_db/data/information_source/annotation.yaml

@@ -0,0 +1,6 @@
+- model: endoreg_db.InformationSource
+  fields:
+    name: "default_annotation"
+    information_source_types: [
+      "annotation"
+    ]

endoreg_db/data/information_source/endoscopy_guidelines.yaml

@@ -0,0 +1,7 @@
+- model: endoreg_db.InformationSource
+  fields:
+    name: "guideline_quality_in_gi"
+    name_de: "Qualitätsanforderungen in der gastrointestinalen Endoskopie v2.0"
+    name_en: "Quality requirements in gastrointestinal endoscopy v2.0"
+    date: "2025-01-01" # not final
+    #TODO Implement information_source

endoreg_db/data/information_source/prediction.yaml

@@ -0,0 +1,7 @@
+- model: endoreg_db.InformationSource
+  fields:
+    name: "default_prediction"
+    information_source_types: [
+      "prediction"
+    ]
+